The high-quality development of energy is closely related to the efficiency of energy utilization, and improving the hydraulic performance of the pump as turbine ( PAT ) has become increasingly important. In order to explore the influence mechanism of the clocking effect on the hydraulic performance of the pump as turbine, the energy loss analysis method based on entropy production theory is used to explore its hydraulic performance and internal flow characteristics. The results show that the clocking effect has an impact on the pump as turbine at all flow rates. Compared to the initial scheme, the efficiency of the C6 scheme is improved by 1.60% and 1.93% at the design and overload conditions. With the increase of the guide vane clocking angle, the flow field near the tongue and guide vane is improved, and the loss of the vortices in the volute is weakened, which in turn improves the hydraulic performance of the PAT. The effect of the clocking effect on pressure pulsation at low flow rates is more significant, and the C6 scheme has the best pressure pulsation characteristics. The research in this paper reveals the cause of the clocking effect, which can provide a theoretical basis for the hydraulic optimization of the pump as turbine.